Effect of Temperature on the Structure and Phase Behavior of Water Confined by Hydrophobic, Hydrophilic, and Heterogeneous Surfaces

Confinement Effects on Reorientation Dynamics of Water Confined within Graphite Nanoslits

Molecular dynamics simulations were used to investigate the reorientation dynamics of water confined within graphite nanoslits of size less than 2 nm, where molecules formed inner and interfacial layers parallel to the confining walls. Significantly related to molecular reorientations, the hydrogen-bond (HB) network of nanoconfined water therein was scrutinized by HB configuration fractions compared to those of bulk water and the influences on interfacial-molecule orientations relative to a nearby C atom plate. The second-rank orientation time correlation functions (OTCFs) of nanoconfined water were calculated and found to follow stretched-exponential, power-law, and power-law decays in a time series. To understand this naïve behavior of reorientation relaxation, the approach of statistical mechanics was adopted in our studies. In terms of the orientation Van Hove function (OVHF), an alternative meaning was given to the second-rank OTCF, which is a measure of the deviation of the OVHF between a molecular system and free molecules in random orientations. Indicated by the OVHFs at related time scales, the stretched-exponential decay of the second-rank OTCF resulted from molecules evacuating out of HB cages formed by their neighbors. After the evacuations, the inner molecules relaxed at relatively fast rates toward random orientations, but the interfacial molecules reoriented at slow rates due to restrictions by hydrophobic interactions with graphite walls. The first power-law decay of the second-rank OTCF was attributed to the distinct relaxation rates of inner and interfacial molecules within a graphite nanoslit. When the inner molecules were completely random in orientation, the second-rank OTCFs changed to another power law decay with a power smaller than the first one.

Mapping Protein-Protein Interactions at Birth: Single-Particle Cryo-EM Analysis of a Ribosome-Nascent Globin Complex

Interactions between ribosome-bound nascent chains (RNCs) and ribosomal components are critical to elucidate the mechanism of cotranslational protein folding. Nascent protein-ribosome contacts within the ribosomal exit tunnel were previously assessed mostly in the presence of C-terminal stalling sequences, yet little is known about contacts taking place in the absence of these strongly interacting motifs. Further, there is nearly no information about ribosomal proteins (r-proteins) interacting with nascent chains within the outer surface of the ribosome. Here, we combine chemical cross-linking, single-particle cryo-EM, and fluorescence anisotropy decays to determine the structural features of ribosome-bound apomyoglobin (apoMb). Within the ribosomal exit tunnel core, interactions are similar to those identified in previous reports. However, once the RNC enters the tunnel vestibule, it becomes more dynamic and interacts with ribosomal RNA (rRNA) and the L23 r-protein. Remarkably, on the outer surface of the ribosome, RNCs interact mainly with a highly conserved nonpolar patch of the L23 r-protein. RNCs also comprise a compact and dynamic N-terminal region lacking contact with the ribosome. In all, apoMb traverses the ribosome and interacts with it via its C-terminal region, while N-terminal residues sample conformational space and form a compact subdomain before the entire nascent protein sequence departs from the ribosome.

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

Management of the poultry red mite Dermanyssus gallinae with physical control methods by inorganic material and future perspectives

Poultry red mite (PRM), the ectoparasitic mite Dermanyssus gallinae found in laying hen farms, is a significant threat to poultry production and human health worldwide. It is a suspected disease vector and attacks hosts' other than chickens, including humans, and its economic importance has increased greatly. Different strategies to control PRM have been widely tested and investigated. In principle, several synthetic pesticides have been applied to control PRM. However, recent alternative control methods to avoid the side effects of pesticides have been introduced, although many remain in the early stage of commercialization. In particular, advances in material science have made various materials more affordable as alternatives for controlling PRM through physical interactions between PRM. This review provides a summary of PRM infestation, and then includes a discussion and comparison of different conventional approaches: 1) organic substances, 2) biological approaches, and 3) physical inorganic material treatment. The advantages of inorganic materials are discussed in detail, including the classification of materials, as well as the physical mechanism-induced effect on PRM. In this review, we also consider the perspective of using several synthetic inorganic materials to suggest novel strategies for improved monitoring and better information regarding treatment interventions.

Liquid-Liquid Phase Separation? Ask the Water!

Water is more than an inert spectator during liquid-liquid phase separation (LLPS), the reversible compartmentalization of protein solutions into a protein-rich and a dilute phase. We show that LLPS is driven by changes in hydration entropy and enthalpy. Tuning LLPS by adjusting experimental parameters, e.g., addition of co-solutes, is a major goal for biological and medical applications. This requires a general model to quantify thermodynamic driving forces. Here, we develop such a model based on the measured amplitudes of characteristic THz-features of two hydration populations: "Cavity-wrap" water hydrating hydrophobic patches is released during LLPS leading to an increase in entropy. "Bound" water hydrating hydrophilic patches is retained since it is enthalpically favorable. We introduce a THz-phase diagram mapping these spectroscopic/thermodynamic changes. This provides not only a precise understanding of hydrophobic and hydrophilic hydration driving forces as a function of temperature and concentration but also a rational means to tune LLPS.

Confinement Dynamics of Nanodroplets between Two Surfaces: Effects of Wettability and Electric Field

The electrowetting effect and related applications of tiny droplets have aroused widespread research interest. In this work, we report molecular dynamics simulations of confinement dynamics of nanodroplets under different droplet-surface interactions and surface distances under an external electric field. So far, the effect of the surface-droplet interactions on electric field-induced dynamics behaviors of droplets in confined spaces has not been extensively studied. Our results show that in the absence of electric field there is a critical value of surface wettability for the shape transition of droplets. Above this value, the droplet is divided into small droplets adhered on the bottom and top surfaces; below this value, the droplets are detached from the surfaces. When an external electric field is applied parallel to the surfaces, the droplet spreads on the surface along the direction of the electric field. It was found that the surface separation significantly influences the transition of the droplet shape. The steady morphology of the droplets under the electric field depends on the surface-droplet interaction and surface separation. We explore the underlying mechanism causing the morphological transition through analyzing the molecular interactions, the number of interracial molecules and the interaction force between the droplets and surfaces. These results provide basic insights into the molecular interactions of nanodroplets under different confined environments, and clues for applications of confined nanodroplets under the control of electric field.

Using Metadynamics To Explore the Free Energy of Dewetting in Biologically Relevant Nanopores

Water confined within hydrophobic spaces can undergo cooperative dewetting transitions due to slight changes in water density and pressure that push water toward the vapor phase. Many transmembrane protein ion channels contain nanoscale hydrophobic pores that could undergo dewetting transitions, sometimes blocking the flow of ions without physical blockages. Standard molecular dynamics simulations have been extensively applied to study the behavior of water in nanoscale pores, but the large free energy barriers of dewetting often prevent direct sampling of both wet and dry states and quantitative studies of the hydration thermodynamics of biologically relevant pores. Here, we describe a metadynamics protocol that uses the number of waters within the pore as the collective variable to drive many reversible transitions between relevant hydration states and calculate well-converged free energy profiles of pore hydration. By creating model nanopore systems and changing their radius and morphology and including various cosolvents, we quantify how these pore properties and cosolvents affect the dewetting transition. The results reveal that the dewetting free energy of nanoscale pores is determined by two key thermodynamic parameters, namely, the effective surface tension coefficients of water-air and water-pore interfaces. Importantly, while the effect of salt can be fully captured in the water activity dependence, amphipathic cosolvents such as alcohols modify both dry and wet states of the pore and dramatically shift the wet-dry equilibrium. The metadynamics approach could be applied to studies of dewetting transitions within nanoscale pores of proteins and provide new insights into why different pore properties evolved in biological systems.

Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain

Hydration free energies are dictated by a subtle balance of hydrophobic and hydrophilic interactions. We present here a spectroscopic approach, which gives direct access to the two main contributions: Using THz-spectroscopy to probe the frequency range of the intermolecular stretch (150-200 cm-1 ) and the hindered rotations (450-600 cm-1 ), the local contributions due to cavity formation and hydrophilic interactions can be traced back. We show that via THz calorimetry these fingerprints can be correlated 1 : 1 with the group specific solvation entropy and enthalpy. This allows to deduce separately the hydrophobic (i.e. cavity formation) and hydrophilic contributions to thermodynamics, as shown for hydrated alcohols as a case study. Accompanying molecular dynamics simulations quantitatively support our experimental results. In the future our approach will allow to dissect hydration contributions in inhomogeneous mixtures and under non-equilibrium conditions.

Different Temperature- and Pressure-Effects on the Water-Mediated Interactions between Hydrophobic, Hydrophilic, and Hydrophobic-Hydrophilic Nanoscale Surfaces

Water-mediated interactions (WMI) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic-hydrophilic) interactions have been mostly overlooked. Here we study the role of T and P of the WMI between nanoscale (i) hydrophobic-hydrophobic, (ii) hydrophilic-hydrophilic, and (iii) hydrophilic-hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic and hybrid interactions are all sensitive to P. However, while hydrophobic interactions [case (i)] are sensitive to T-variations, hydrophilic [case (ii)] and hybrid interactions [case (iii)] are practically T-independent. An analysis of the entropic and enthalpic contributions to the PMF for cases (i)-(iii) is also presented. Our results are important in understanding T- and P-induced protein denaturation, and the interactions of biomolecules in solution, including protein aggregation andphase separation processes. From the computational point of view, the results presented here are relevant in the design of implicit water models for the study of molecular and colloidal/nanoparticle systems at different thermodynamic conditions.

A molecular simulation study into the stability of hydrated graphene nanochannels used in nanofluidics devices

Graphene-based nanochannels are a popular choice in emerging nanofluidics applications because of their tunable and nanometer-scale channels. In this work, molecular dynamics (MD) simulations were employed both to (i) assess the stability of dry and hydrated graphene nanochannels and (ii) elucidate the properties of water confined in these channels, using replica-scale models with 0.66-2.38 nm channel heights. The use of flexible nanochannel walls allows the nanochannel height to relax in response to the solvation forces arising from the confined fluid and the forces between the confining surfaces, without the need for application of arbitrarily high external pressures. Dry nanochannels were found to completely collapse if the initial nanochannel height was less than 2 nm, due to attractive van der Waals interactions between the confining graphene surfaces. However, the presence of water was found to prevent total nanochannel collapse, due to repulsive hydration forces opposing the attractive van der Waals force. For nanochannel heights less than ∼1.7 nm, the confining surfaces must be relaxed to obtain accurate hydration pressures and water diffusion coefficients, by ensuring commensurability between the number of confined water layers and the channel height. For very small (∼0.7 nm), hydrated channels a pressure of 231 MPa due to the van der Waals forces was obtained. In the same system, the confined water forms a mobile, liquid monolayer with a diffusion coefficient of 4.0 × 10^-5 cm² s^-1, much higher than bulk liquid water. Although this finding conflicts with most classical MD simulations, which predict in-plane order and arrested dynamics, it is supported by experiments and recently published first-principles MD simulations. Classical simulations can therefore be used to predict the properties of water confined in sub-nanometre graphene channels, providing sufficiently realistic molecular models and accurate intermolecular potentials are employed.

Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids

Nanoconfinement can drastically change the behavior of liquids, puzzling us with counterintuitive properties. It is relevant in applications, including decontamination and crystallization control. However, it still lacks a systematic analysis for fluids with different bulk properties. Here we address this gap. We compare, by molecular dynamics simulations, three different liquids in a graphene slit pore: (1) A simple fluid, such as argon, described by a Lennard-Jones potential; (2) an anomalous fluid, such as a liquid metal, modeled with an isotropic core-softened potential; and (3) water, the prototypical anomalous liquid, with directional HBs. We study how the slit-pore width affects the structure, thermodynamics, and dynamics of the fluids. All the fluids show similar oscillating properties by changing the pore size. However, their free-energy minima are quite different in nature: (i) are energy-driven for the simple liquid; (ii) are entropy-driven for the isotropic core-softened potential; and (iii) have a changing nature for water. Indeed, for water, the monolayer minimum is entropy driven, at variance with the simple liquid, while the bilayer minimum is energy driven, at variance with the other anomalous liquid. Also, water has a large increase in diffusion for subnm slit pores, becoming faster than bulk. Instead, the other two fluids have diffusion oscillations much smaller than water, slowing down for decreasing slit-pore width. Our results, clarifying that water confined at the subnm scale behaves differently from other (simple or anomalous) fluids under similar confinement, are possibly relevant in nanopores applications, for example, in water purification from contaminants.

Structure of the Water Molecule Layer between Ice and Amorphous/Crystalline Surfaces Based on Molecular Dynamics Simulations

The structure of the water layer between the ice interface and the hydroxylated amorphous/crystalline silica surfaces was investigated using molecular dynamics simulations. The results indicate that the density profile in the direction perpendicular to the surface has two density peaks in the water layer at the ice-silica interface, which are affected by the silanol group density on the wall and the degree of supercooling in the system. In the two density peaks, the one facing the ice interface side has the same structure as the ice crystal, while the other density peak facing the silica surface has an icelike structure. In the solidification process, the ice and icelike structures in the layer progress more on the amorphous silica surface where the density of the silanol groups is low. The relationship between the ice crystallization and the thickness of the layer has been studied in detail; the lower the temperature, the more the ice crystallization progresses and the thinner the layer becomes.

Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction

Although it is well-known that limited local mutations of enzymes, such as matrix metalloproteinases (MMPs), may change enzyme activity by orders of magnitude as well as its stability, the completely rational design of proteins is still challenging. These local changes alter the electrostatic potential and thus local electrostatic fields, which impacts the dynamics of water molecules close the protein surface. Here we show by a combined computational design, experimental, and molecular dynamics (MD) study that local mutations have not only a local but also a global effect on the solvent: In the specific case of the matrix metalloprotease MMP14, we found that the nature of local mutations, coupled with surface morphology, have the ability to influence large patches of the water hydrogen-bonding network at the protein surface, which is correlated with stability. The solvent contribution can be experimentally probed via terahertz (THz) spectroscopy, thus opening the door to the exciting perspective of rational protein design in which a systematic tuning of hydration water properties allows manipulation of protein stability and enzymatic activity.

Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels

Water is at the heart of almost all biological phenomena, without which no life that we know of would have been possible. It is a misleadingly complex liquid that exists in near coexistence with the vapor phase under ambient conditions. Confinement within a hydrophobic cavity can tip this balance enough to drive a cooperative dewetting transition. For a nanometer-scale pore, the dewetting transition leads to a stable dry state that is physically open but impermeable to ions. This phenomenon is often referred to as hydrophobic gating. Numerous transmembrane protein ion channels have now been observed to utilize hydrophobic gating in their activation and regulation. Here, we review recent theoretical, simulation, and experimental studies that together have started to establish the principles of hydrophobic gating and discuss how channels of various sizes, topologies, and biological functions can utilize these principles to control the thermodynamic properties of water within their interior pores for gating and regulation. Exciting opportunities remain in multiple areas, particularly on direct experimental detection of hydrophobic dewetting in biological channels and on understanding how the cell may control the hydrophobic gating in regulation of ion channels.

Molecular Fingerprints of Hydrophobicity at Aqueous Interfaces from Theory and Vibrational Spectroscopies

Hydrophobicity/hydrophilicity of aqueous interfaces at the molecular level results from a subtle balance in the water-water and water-surface interactions. This is characterized here via density functional theory-molecular dynamics (DFT-MD) coupled with vibrational sum frequency generation (SFG) and THz-IR absorption spectroscopies. We show that water at the interface with a series of weakly interacting materials is organized into a two-dimensional hydrogen-bonded network (2D-HB-network), which is also found above some macroscopically hydrophilic silica and alumina surfaces. These results are rationalized through a descriptor that measures the number of "vertical" and "horizontal" hydrogen bonds formed by interfacial water, quantifying the competition between water-surface and water-water interactions. The 2D-HB-network is directly revealed by THz-IR absorption spectroscopy, while the competition of water-water and water-surface interactions is quantified from SFG markers. The combination of SFG and THz-IR spectroscopies is thus found to be a compelling tool to characterize the finest details of molecular hydrophobicity at aqueous interfaces.

Insignificant Effect of Temperature on the Structure and Angular Jumps of Water near a Hydrophobic Cation

The ambiguity in the behavior of water molecules around hydrophobic solutes is a matter of interest for many studies. Motivated by the earlier results on the dynamics of water molecules around tetramethylammonium (TMA) cation, we present the effect of temperature on the structure and angular jumps of water due to hydrophobicity using first principles molecular dynamics simulations. The average intermolecular distance between the central oxygen and four nearest neighbors is found to be the highest for water molecules in the solvation shell of TMA at 400 K, followed by the same at 330 K. The hydrogen bond (HB) donor-acceptor count, HB per water molecule, and tetrahedral order parameter suggests the loss of tetrahedrality in the solvation shell. Elevated temperature affects the tetrahedral parameter in local regions. The HB jump mechanism is studied for methyl hydrogen and water molecules in the solvation shell. Observations hint at the presence of dangling water molecules in the vicinity of the hydrophobic cation, and no evidence is found for the enhanced structural ordering of nearby water molecules.

Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution

Performance of membranes for water purification is highly influenced by the interactions of solvated species with membrane surfaces, including surface adsorption of solutes upon fouling. Current efforts toward fouling-resistant membranes often pursue surface hydrophilization, frequently motivated by macroscopic measures of hydrophilicity, because hydrophobicity is thought to increase solute-surface affinity. While this heuristic has driven diverse membrane functionalization strategies, here we build on advances in the theory of hydrophobicity to critically examine the relevance of macroscopic characterizations of solute-surface affinity. Specifically, we use molecular simulations to quantify the affinities to model hydroxyl- and methyl-functionalized surfaces of small, chemically diverse, charge-neutral solutes represented in produced water. We show that surface affinities correlate poorly with two conventional measures of solute hydrophobicity, gas-phase water solubility and oil-water partitioning. Moreover, we find that all solutes show attraction to the hydrophobic surface and most to the hydrophilic one, in contrast to macroscopically based hydrophobicity heuristics. We explain these results by decomposing affinities into direct solute interaction energies (which dominate on hydroxyl surfaces) and water restructuring penalties (which dominate on methyl surfaces). Finally, we use an inverse design algorithm to show how heterogeneous surfaces, with multiple functional groups, can be patterned to manipulate solute affinity and selectivity. These findings, importantly based on a range of solute and surface chemistries, illustrate that conventional macroscopic hydrophobicity metrics can fail to predict solute-surface affinity, and that molecular-scale surface chemical patterning significantly influences affinity-suggesting design opportunities for water purification membranes and other engineered interfaces involving aqueous solute-surface interactions.

A Deep Look into the Dynamics of Saltwater Imbibition in a Calcite Nanochannel: Temperature Impacts Capillarity Regimes

This research concerns fundamentals of spontaneous transport of saltwater (1 mol·dm^-3 NaCl solution) in nanopores of calcium carbonates. A fully atomistic model was adopted to scrutinize the temperature dependence of flow regimes during solution transport under CaCO₃ nanoconfinement. The early time of capillary filling is inertia-dominated, and the solution penetrates with a near-planar meniscus at constant velocity. Following a transition period, the meniscus angle falls to a stabilized value, characterizing the capillary-viscous advancement in the calcite channel. At this stage, brine displacement follows a parabolic relationship consistent with the classical Lucas-Washburn (LW) theory. Approaching the slit outlet, the meniscus contact lines spread widely on the solid substrate and brine leaves the channel at a constant rate, in oppose to the LW law. The brine imbibition rate considerably increases at higher temperatures as a result of lower viscosity and greater tendency to form wetting layers on slit walls. We also pointed out a longer primary inertial regime and delayed onset of the viscous-capillary regime at higher temperatures. Throughout the whole span of capillary displacement, transport of sodium and chloride ions is tied to dynamics and diffusion of the water phase, even at the mineral interface. The results presented in this study are of broad implications in diverse science and technological applications.

Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces

The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.

Structure and sum-frequency generation spectra of water on uncharged Q4 silica surfaces: a molecular dynamics study

The structural characteristics and sum-frequency generation (SFG) spectra of water near neutral Q₄ silica surfaces were investigated by molecular dynamics simulations. The interactions of water molecules with atoms of the solid were described by different potential models, in particular by the CLAYFF [Cygan et al., J. Phys. Chem. B, 2004, 108, 1255] and INTERFACE [Heinz et al. Langmuir, 2013, 29, 1754] force fields. The calculations of the contact angle of water have shown that the silica surface modeled with CLAYFF behaves as macroscopically hydrophilic, in contrast to the surface described with the INTERFACE model. The hydrophilicity of CLAYFF stems from too attractive electrostatic surface-water interactions. Regardless of the surface's affinity for water, the aqueous phase has a layered structure in the direction perpendicular to the surface with density fluctuations decaying within a distance of 10 Å from the surface. The orientational ordering of H₂O molecules was found to be more short-range than the density fluctuations, especially for the hydrophobic surfaces. Modeling the SFG spectra has shown that the spectra of all studied hydrophobic silica-water interfaces are similar and have features in common with the spectrum of the water-vapor interface. The spectra fairly agree with experimental results obtained for the silica-water interface at low pH conditions [Myalitsin et al., J. Phys. Chem. C, 2016, 120, 9357]. The spectral response for the hydrophobic interface was computed to primarily arise from the topmost molecules of the first layer of interfacial water. In contrast, the SFG signal from the hydrophilic silica-water interface is accumulated over a greater distance extending for several water layers due to more long-range perturbation of the structure by the surface.

Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering

Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.

Role of Water Hydrogen Bonding on Transport of Small Molecules inside Hydrophobic Channels

We conducted a systematic analysis of water networking inside smooth hyperboloid hydrophobic structures (cylindrical, barrel, and hourglass shapes) to elucidate the role of water hydrogen bonding on the transport of small hydrophobic molecules (ligands). Through a series of molecular dynamics simulations, we established that a hydrogen-bonded network forming along the centerline resulted in a water exclusion zone adjacent to the walls. The size of the exclusion zone is a function of the geometry and the nonbonded interaction strength, defining the effective hydrophobicity of the structure. Exclusion of water molecules from this zone results in lower apparent viscosity, leading to acceleration of ligand transport up to 7 times faster than that measured in the bulk. Transport of ligands into and out of the hydrophobic structures was shown to be controlled by a single water molecule that capped the narrow regions in the structure. This mechanism provides physical insights into the behavior and role of water in the bottleneck regions of hydrophobic enzyme channels. These findings were then used in a sister publication [ Escalante , D. E. , Comput. Struct. Biotechnol. J. 2019 17 757 760 ] to develop a model that can accurately predict the transport of ligands along nanochannels of broad-substrate specificity enzymes.

Molecular dynamics simulations of nano-confined methanol and methanol-water mixtures between infinite graphite plates: Structure and dynamics

Molecular dynamics simulations are used to investigate microscopic structures and dynamics of methanol and methanol-water binary mixture films confined between hydrophobic infinite parallel graphite plate slits with widths, H, in the range of 7-20 Å at 300 K. The initial geometric densities of the liquids were chosen to be the same as bulk methanol at the same temperature. For the two narrowest slit widths, two smaller initial densities were also considered. For the nano-confined system with H = 7 Å and high pressure, a solid-like hexagonal arrangement of methanol molecules arranged perpendicular to the plates is observed which reflects the closest packing of the molecules and partially mirrors the structure of the underlying graphite structure. At lower pressures and for larger slit widths, in the contact layer, the methanol molecules prefer having the C-O bond oriented parallel to the walls. Layered structures of methanol parallel to the wall were observed, with contact layers and additional numbers of central layers depending on the particular slit width. For methanol-water mixtures, simulations of solutions with different composition were performed between infinite graphite slits with H = 10 and 20 Å at 300 K. For the nanoslit with H = 10 Å, in the solution mixtures, three layers of molecules form, but for all mole fractions of methanol, methanol molecules are excluded from the central fluid layer. In the nanopore with H = 20 Å, more than three fluid layers are formed and methanol concentrations are enhanced near the confining plates walls compared to the average solution stoichiometry. The self-diffusion coefficients of methanol and water molecules in the solution show strong dependence on the solution concentration. The solution mole fractions with minimal diffusivity are the same in confined and non-confined bulk methanol-water mixtures.

Tunable surface adsorption and wettability of candle soot coated on ferroelectric ceramics

A ferroelectric Ba0.85Ca0.15Ti0.9Zr0.1O3 (BCZTO) ceramic was prepared using a solid-state reaction route. A coating of candle soot was provided on poled and unpoled BCZTO samples. X-ray diffraction and Raman spectroscopy confirmed the presence of the graphite form of carbon in the candle soot. Scanning Kelvin probe microscopy determined that the highest surface potentials were ∼34 mV and 1.5 V in the unpoled and poled BCZTO samples, respectively. The candle soot was found to adsorb ∼65%, 80%, and 90% of the methylene blue dye present in acidic, neutral, and basic media, respectively, within 3 h. In both the poled and unpoled cases, the BCZTO samples coated with candle soot showed greater adsorption capacities than the uncoated BCZTO sample. In the cases of poled samples coated with candle soot, the adsorption was found to be greater in the case of candle soot coated on a positively charged surface than that for candle soot coated on a negatively charged BCZTO surface in an acidic medium. In a basic medium, the adsorption was found to be greater in the case of candle soot coated on a negatively charged surface than that for candle soot coated on a positively charged BCZTO surface. The contact angle of the candle soot-coated BCZTO sample was found to be hydrophobic (∼149°). The contact angle decreased (∼149-133°) with an increase in temperature (30-70 °C) in the case of candle soot coated on the positive surface of a poled BCZTO sample. The contact angle increased (∼139-149°) with an increase in temperature (30-70 °C) in the case of candle soot coated on the negative surface of a poled BCZTO sample. Internal electric field-assisted (associated with ferroelectric materials) adsorption could be a potential technique to improve adsorption processes.

Study of distance dependence of hydrophobic force between two graphene-like walls and a signature of pressure induced structure formation in the confined water

We examine the separation distance dependence of the hydrophobic force by systematically varying the distance (d) between two walls. The hydrophobic force exhibits a distance mediated crossover from a liquid-like to a gas-like behavior at around d ∼ 12 Å for 1 atm pressure. The distance dependence can be fitted to a bi-exponential form, with the longer distance part displaying a correlation length of 20 Å. In addition, the crossover is found to be accompanied by a divergent-like growth of the local relative number fluctuation of the water molecules confined between the two surfaces. Furthermore, at a fixed separation (d = 20 Å), we observe a pressure induced structural modification of confined water at high pressure. The confined water is found to form an ordered structure at high pressure (10 000 atm) and room temperature, in agreement with the experimental study [G. Algara-Siller et al. Nature 519(7544), 443 (2015)].

Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly

De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign of the protein surface with conditionally repulsive electrostatic interactions enabled us to predictably perturb the free-energy landscape and obtain a new protein lattice whose conformational dynamics can be chemically and mechanically toggled between three different states with varying porosities and molecular densities.

Dynamics and structural behavior of water in large confinement with planar amorphous walls

We study the structure and dynamics of liquid water confined between planar amorphous walls using molecular dynamics (MD) simulations. We report MD results for systems of more than 23 000 SPC/E water molecules confined between two hydrophilic or hydrophobic walls, separated by distances of about 15 nm. We find that the walls induce ordering of the liquid and slow down the dynamics, affecting the properties of the confined water up to distances of about 8 nm at 275 K. We quantify this influence by computing dynamic and static penetration lengths and studying their temperature dependence. Our results indicate that in the temperature range considered, hydrophobic walls perturb static properties over larger lengths compared to hydrophilic walls. We also find opposite temperature trends in the dynamic penetration lengths, with hydrophobic walls increasing their range of influence on increasing the temperature.

Structure and mobility of water confined in AlPO4-54 nanotubes

We performed molecular dynamics simulations of water confined within AlPO₄-54 nanotubes. AlPO₄-54 is an artificial material made of AlO₄ and of PO₄ in tetrahedra arranged in a periodic structure forming pores of approximately 1.3 nm in diameter. This makes AlPO₄-54 an excellent candidate for practical applications, such as for water filtration and desalination. In this work, the structural and dynamical properties of the confined water are analyzed for various temperatures and water loadings. We find that the water structure is controlled by the heterogeneity of the nanopore surface with the water molecules located preferentially next to the surface of oxygens of AlPO₄-54; consequently, at very low densities, water forms helicoidal structures in string-like arrangements.

Effects of confinement between attractive and repulsive walls on the thermodynamics of an anomalous fluid

We study via molecular-dynamics simulations the thermodynamics of an anomalous fluid confined in a slit pore with one wall structured and attractive and another unstructured and repulsive. We find that the phase diagram of the homogeneous part of the confined fluid is shifted to higher temperatures, densities, and pressures with respect to the bulk, but it can be rescaled on the bulk case. We calculate a moderate increase of mobility of the homogeneous confined fluid that we interpret as a consequence of the layering due to confinement and the collective modes due to long-range correlations. We show that, as in bulk, the confined fluid has structural, diffusion, and density anomalies that order in the waterlike hierarchy, and a liquid-liquid critical point (LLCP). The overall anomalous region moves to higher temperatures, densities, and pressure, and the LLCP displaces to higher temperature compared to bulk. Motivated by experiments, we calculate also the phase diagram not just for the homogeneous part of the confined fluid but for the entire fluid in the pore, and we show that it is shifted toward higher pressures but preserves the thermodynamics, including the LLCP. Because our model has waterlike properties, we argue that in experiments with supercooled water confined in slit pores with a width of >3 nm if hydrophilic and of >1.5 nm if hydrophobic, the existence of the LLCP could be easier to test than in bulk, where it is not directly accessible.

The Carbon-Water Interface: Modeling Challenges and Opportunities for the Water-Energy Nexus

Providing clean water and sufficient affordable energy to all without compromising the environment is a key priority in the scientific community. Many recent studies have focused on carbon-based devices in the hope of addressing this grand challenge, justifying and motivating detailed studies of water in contact with carbonaceous materials. Such studies are becoming increasingly important because of the miniaturization of newly proposed devices, with ubiquitous nanopores, large surface-to-volume ratio, and many, perhaps most of the water molecules in contact with a carbon-based surface. In this brief review, we discuss some recent advances obtained via simulations and experiments in the development of carbon-based materials for applications in water desalination. We suggest possible ways forward, with particular emphasis on the synergistic combination of experiments and simulations, with simulations now sometimes offering sufficient accuracy to provide fundamental insights. We also point the interested reader to recent works that complement our short summary on the state of the art of this important and fascinating field.

Strong Coupling between Nanofluidic Transport and Interfacial Chemistry: How Defect Reactivity Controls Liquid-Solid Friction through Hydrogen Bonding

Defects are inevitably present in nanofluidic systems, yet the role they play in nanofluidic transport remains poorly understood. Here, we report ab initio molecular dynamics (AIMD) simulations of the friction of liquid water on defective graphene and boron nitride sheets. We show that water dissociates at certain defects and that these "reactive" defects lead to much larger friction than the "nonreactive" defects at which water molecules remain intact. Furthermore, we find that friction is extremely sensitive to the chemical structure of reactive defects and to the number of hydrogen bonds they can partake in with the liquid. Finally, we discuss how the insight obtained from AIMD can be used to quantify the influence of defects on friction in nanofluidic devices for water treatment and sustainable energy harvesting. Overall, we provide new insight into the role of interfacial chemistry on nanofluidic transport in real, defective systems.

Density of hydrophobically confined deeply cooled water investigated by small angle X-ray scattering

Water's behavior near hydrophobic surfaces has attracted great attention due to chemical and geological applications. Here, we report small angle X-ray scattering (SAXS) studies of water confined in the hydrophobic nanoporous carbon material, CMK-1-14, from ambient to deeply cooled temperatures. By monitoring the scattering intensity of the first Bragg peak, which is directly related to the scattering length density contrast between the carbon matrix and the confined water, the average density of the hydrophobically confined water was determined from 300 K to 150 K at ambient pressure. Furthermore, differential scanning calorimetry and X-ray diffraction measurements showed that the majority of such hydrophobically confined water did not crystallize in the investigated temperature range. By exploiting the fast speed of SAXS measurements and the continuous temperature ramping, the average density profile and the deduced thermal expansion coefficient (αp) were obtained. We found that the well-known density maximum of water at 277 K downshifted to 260 K, and the density minimum which has been observed in hydrophilic confinement disappeared. In addition, the previously measured large density decreasing of 18% at low temperature was recalibrated to a more reasonable 10% instead. Consequently, the recalculated αp peak was found to be quite similar to that of the water confined in hydrophilic MCM-41-S-15 suggesting an intrinsic property of water, which does not sensitively depend on the confinement surface.

Characterization of the Local Structure in Liquid Water by Various Order Parameters

A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism.